Shy Guy ships are flying away from Pipe Land. One ship is carrying Mario, Luigi, Wario, Waluigi, Bowser Jr, Lewis and General Guy.
Mario: What will we do? The Koopas won’t leave us alone until Bowser has Bowser Jr. dead or back at his castle.
Bowser Jr: I must go find Bowser and face him alone.
Mario: No, it’s too dangerous! Me, Luigi, and the Wario Bros. can handle him.
Luigi: I don’t think that’s a good idea because the doomship is chasing us.
Wario: Waluigi, stick to me! I have a plan!
Waluigi: I have a feeling it won’t work!
The doomship sends down minions and fires Bullet Bills at the Shy Guy ships.
General Guy: All ships report! Start a ground pursuit. We need to find Bowser.
Several Shy Guy ships land and Shy Guys attack Goombas, Koopa Troopas, Hammer Bros, Koopa Paratroopas, and Magikoopas.
Mario: Lewis! Send an air pursuit.
Lewis: Yes sir!
Lewis and some Shy Guy ships attack the doomships. Mario follows the main doomship, while Wario and Waluigi lead forces. Wario ground pounds some Goombas and Koopa Troopas, and Waluigi throws Bob ombs at the Hammer Bros. and Magikoopas. Lewis destroys some doomships. On the main doomship, Bowser takes an escape pod while Ludwig and Larry watch the battle through the screen.
Ludwig: We have to order a retreat.
Larry: You might be right. We have to send the remaining minions into battle. I’m going to leave now.
Ludwig: Before you go, I must give you the instructions for my ultimate plan. King Dad, the Mario Bros, and our siblings cannot find out, though.
Larry: Understood.
Larry leaves in the escape pod to go to Grass Land. The other Koopalings (except Jr) have gone to their lands. Ludwig remains because he is already in Pipe Land. Mario sees the escape pod with Bowser, but it crashes into Pipe Land’s castle. Mario arrives there in front of a ship to prevent Bowser from escaping.
Mario: Bowser, you won’t escape this time.
Bowser: Ok, maybe not, but instead of fighting regularly, how about we fight an old-fashioned lightsaber battle?
Mario: Very well!
Mario takes a lightsaber out of his pocket and opens it up. His color is blue. Bowser grabs one out of his crown and opens it. His is red. Mario hits Bowser’s regularly with a horizontal slice. Bowser attacks more aggressively as Mario defends and attacks. They move into the castle power plant. Mario starts attacking diagonally while Bowser defends. They move onto a bridge with no rails as they keep slashing at each other’s lightsabers. Mario is caught off-guard as Bowser tries to behead him, but Mario ducks just in time. Mario tries to defend himself more as Bowser’s attacks get more aggressive. Bowser backflips onto a ledge, Mario jumps onto the same ledge that Bowser is on. Mario has to attack more aggressively as Bowser gets more aggressive. Mario keeps hitting Bowser’s saber and eventually knocks him into a pit, but Bowser grabs Mario’s leg, causing him to fall too. Mario kicks Bowser as they fall but Bowser punches Mario as they hit the floor. Bowser grabs his saber and tries to throw it at Mario, but he misses and hits the main power generator in the castle, causing it to lose power. Bowser then grabs his saber and they continue to battle even though the ceiling is falling apart.
Meanwhile, Luigi and Lewis are destroying Koopas until they hear Ludwig’s voice thoughout the doomship.
Ludwig: Ok Sky Guys, you win this one, but we’ll be back!
Luigi: We have to save Mario! Lewis, get Wario, Waluigi, General Guy, and Jr!
Lewis: I will!
Meanwhile, Bowser and Mario are still at it. Bowser is attacking less aggressively because he is getting tired from all the fighting. He keeps fighting as Mario keeps slashing his saber with Bowser defending with his until they enter a struggle. Bowser then kicks Mario, knocking him into the basement of the castle. Bowser follows Mario, ignoring a sign that says “Danger - Nuclear Bob-omb”. Mario gets up and grabs his saber and strikes Bowser’s saber until they enter another struggle in which Mario kicks Bowser, knocking him over next to a Bob-omb the size of Lemmy’s Interview studio. Bowser keeps striking Mario with his weapon until Mario kicks him. Bowser gets up but nearly gets his hand cut off. Bowser attacks aggressively again and Mario does too as the duel goes into the cargo hangar. Mario fights to stay alive as he gets weaker, but Bowser does too. They keep fighting as they approach a pit. Mario gets kicked by Bowser and is knocked into the pit. Bowser, sensing Mario isn’t dead, jumps in too. They are now fighting in a factory as the battle gets even more intense. Mario slashes his saber at Bowser, hitting him in the eye, but it only gives him a black eye. He continues even with his lack of vision. Mario grabs a machine and it goes down into a lava pit. Bowser follows Mario and they continue fighting as lava gets on Mario’s overalls. Bowser strikes as aggressively as in the final battle of SMG. Mario throws his hat at Bowser, blinding him momentarily. Mario manages to cut his hand off. He leaves, thinking Bowser is dead. But Bowser sets up a bomb and runs away. Mario sees it and rushes to the entrance.
Ludwig (on the doomship): I’m on my way!
The doomship flies toward Pipe Land’s castle. Luigi, Wario, Waluigi, Bowser Jr, Lewis, and General Guy are there. Bowser comes out with Mario following him.
Bowser: Hurry! The bomb will go off in 15 seconds.
Bowser grabs Jr. and gets on the doomship, avoiding Luigi and the others.
Mario: GET ON THE SHIP!!! IT’S GONNA EXPLODE!!!
Everyone gets on the Shy Guy ship before the castle explodes.
Mario: Head for Peach’s castle!
Shy Guy Pilot: Yes sir!
They head for Peach’s castle.
Previously in our story, the Shy Guys overcame the Koopa forces and won the battle of Pipe Land. Although they won, Bowser escaped with his son Bowser Jr, who was a great general in the war. Until Bowser surrenders the war would continue. This would mark the beginning of the Shy-Koopa War. Princess Peach stood at the entrance of her castle as the veterans returned...
The Shy Guy ship from earlier lands in the courtyard. Out comes Mario, Luigi, Wario, Waluigi, General Guy, and Lewis. Princess Peach welcomes them and walks to the meeting room.
Mario: I have bad news, Princess. The war has begun.
Princess Peach: The war has begun? That’s terrible news to hear.
Luigi: Princess, Bowser has been appointed leader of the Koopa army. Until he is dead or surrenders, I will assure you that war will continue.
Peach: Then who’s our leader?
Mario: All of us standing before you.
They enter the meeting room and sit down.
Peach: We must drive out all his men and take back what we have lost.
They continue to discuss strategy.
Meanwhile in the headquarters of the Koopa army, Castle Koopa, Bowser is on the throne.
Bowser: This is great! The war has begun!
With my newest scheme, bit by bit the kingdom will fall, and soon the princess
will have no choice but to sign over the kingdom.
Ok, this will be a pretty long war. I’ll give you main headquarters and leaders and combatants.
Shy Guy Army
Leaders: General Guy, Lewis, Mario
Bros, Wario Bros.
Main Headquarters: Peach’s Castle
Key Victories: Battle of Pipe Land
Key Losses: None at the time
Fighters: Mario, Luigi, Wario, Waluigi,
General Guy, Lewis, and many other Shy Guys
Koopa Army
Leader: Bowser
Main Headquarters: Castle Koopa
Key Victories: None at the time
Key Losses: Battle of Pipe Land
Fighters: Bowser, the Koopalings, Kamek,
Kammy, Bowser’s army
Mario and the others are still talking.
Mario: We have sighted huge armies, in Ice Land, Thwomp Volcano, Dreadnaught Galaxy, Isle Delfino, Nimbus Land, and Desert Hills.
Luigi: Those are key kingdoms we cannot afford to lose.
Peach: Then we must lead armies to stop them. It will require all of you, so where will each of you go?
Mario: I will go to Dreadnaught Galaxy. I’ll take a fleet and go there.
Luigi: I’ll take care of Ice Land. I’ll come back with a victory, I assure you!
Wario: Leave it to me to ruin their paradise of Isle Delfino.
Waluigi: I’ll go to Thwomp Volcano and burn them all up.
General Guy: I’ll go help Nimbus Land. Besides, Lewis wanted to go to Desert Hills.
Lewis: I always wanted to visit the desert.
Peach: Well, good luck, Generals.
Later Mario and the others arrive at their destinations.
Mario: Look for their leader.
The same thing happens with the other generals. The generals for the Koopas are:
Kamek - Dreadnaught Galaxy
Lemmy - Ice Land
Shadow Mario - Isle Delfino
Commander Shroob - Thwomp Volcano
Smithy - Nimbus Land
Morton - Desert Hills
Mario: Prepare weapons.
Luigi: Prepare weapons.
Wario: Prepare weapons.
Waluigi: Prepare weapons.
General Guy: Prepare weapons.
Lewis: Prepare weapons.
Soon Koopas enter the battlefield and get their weapons out and start firing, as all the battles get intense. Mario jumps at some Hammer Bros. and grab their hammers and pound some Goombas. Shy Guys get blasters and start shooting Koopas with them as they are firing back. Luigi grabs a Fire Flower and shoots fireballs at the nearby ice enemies with Fire Guys at his side; they fry the ice enemies easily. Wario is punching Goombas and Koopa Troopas when he sees a Magikoopa behind him. Wario kicks his wand out of his hand and swipes it. Wario then uses it to brainwash the Koopas, but figures out that this is actually making then stronger and more vicious. He tries to stop them, but it just gets worse until he zaps a Hammer Bro to the size of one of the buildings. Wario panics and runs around. At this point Waluigi hasn’t seen action in battle until Shroob tanks lower out of Shroob UFOS, and then drop Shroids. They sit immobile as, from the main saucer, Commander Shroob is watching.
Commander Shroob: Activate the Shroids.
Shroob Pilot: Yes sir.
The Shroids start to move, pulling up their blaster guns and marching toward the Shy Guy army.
Shroid: Fire!
The Shroids enter the area and both armies begin the battle. Waluigi panics and throws Bob-ombs into the Shroids. Elsewhere, though greatly outnumbered, the Shy Guys continue to fight the battle. General Guy fights robots from Smithy’s Factory. Already armed with his great experience, he gets a blaster out and fires. He hit a few bots and runs to a safe spot and fires. Meanwhile, Lewis fires intensely to the point that he is a threat to the Koopa army. Mario throws a hammer in the window of Kamek’s room in the Dreadnaught. A Shy Guy jumps on a Koopa bot and shoots it down, as more Shy Guys go down. Kamek jumps out of his window and Mario doesn’t hesitate. Luigi jumps on ice enemies as fast as he can until a machine fires extremely cold ice. The ice freezes the Fire Guys to death as it rids them of their flames. It fires more as Luigi rushes to the machine only to see it being operated by Lemmy. Wario is running as fast as he can, punching enemies out of his way, when he finds a huge paint monster that Shadow Mario created. Wario charges at it. Waluigi hits a Shroid with a Bob-omb and kicks one out of his way. He then ducks a laser from a Shroob saucer. He looks to see Commander Shroob throwing Bob-ombs at tanks. Waluigi throws a Bob-omb in the main Shroob saucer. Commander Shroob comes out and is on a Shroob robot. It looks like a giant Shroid but with a cockpit in the eye area. Commander Shroob is inside, controlling the machine. Meanwhile General Guy is forced to abandon his hiding spot and gets in his tank and shoots missiles at the giant robots that look like ants. He throws a Bob-omb at Smithy’s ship. Smithy gets out and throws an electric staff at General Guy’s tank, causing it to explode, leaving General Guy weakened but conscious. Lewis throws a detonator at a desert ship, causing it to explode. Morton then gets his snooze gun and shoots Shy Guys, making them fall asleep. Lewis charges at Morton as the two battle.
Meanwhile, Bowser enters Peach’s castle and makes it to the throne room.
Bowser: Princess Peach! You are to be kidnapped. Plus your friends are about to run into a trap.
Voice in Bowser’s microphone: Sir, the trap has been triggered.
Bowser: Excellent. Proceed with the attack.
Bowser grabs the unarmed and defenseless Princess Peach.
Peach: You won’t get away with this, Bowser!
Bowser takes Peach in his doomship and goes back to Castle Koopa.